Should all applicable controls from Annex A to be fully implemented by the time

Answer: Ideal situation would be to implement all the controls marked as applicable in the Statement of Applicability prior to certification audit.

You could leave less significant controls to be implemented after the certification, under the following conditions: (1) to plan their implementation in the Risk treatment plan, and (2) to accept all the residual risks that were not decreased. There is no magic number on the proportion of how many controls must be implemented, and it is in the certification auditor's discretion to raise a non-conformity in su ch cases. Therefore, to be safe you should implement majority of controls prior to certification audit and make sure you implement all the most important ones.